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- PDB-1rsf: NMR Structure of Monomeric CAR d1 domain -

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Basic information

Entry
Database: PDB / ID: 1rsf
TitleNMR Structure of Monomeric CAR d1 domain
ComponentsCoxsackievirus and adenovirus receptor
KeywordsSIGNALING PROTEIN / CAR / Coxsackievirus / Adenovirus
Function / homology
Function and homology information


AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / gamma-delta T cell activation / regulation of AV node cell action potential / germ cell migration / apicolateral plasma membrane / cell-cell junction organization ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / gamma-delta T cell activation / regulation of AV node cell action potential / germ cell migration / apicolateral plasma membrane / cell-cell junction organization / transepithelial transport / connexin binding / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / bicellular tight junction / intercalated disc / mitochondrion organization / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / filopodium / PDZ domain binding / Cell surface interactions at the vascular wall / adherens junction / neuromuscular junction / beta-catenin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / integrin binding / virus receptor activity / cell junction / cell body / heart development / growth cone / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / neuron projection / membrane raft / signaling receptor binding / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coxsackievirus and adenovirus receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJiang, S. / Jacobs, A. / Laue, T.M. / Caffrey, M.
CitationJournal: Biochemistry / Year: 2004
Title: Solution structure of the coxsackievirus and adenovirus receptor domain 1.
Authors: Jiang, S. / Jacobs, A. / Laue, T.M. / Caffrey, M.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coxsackievirus and adenovirus receptor


Theoretical massNumber of molelcules
Total (without water)13,8151
Polymers13,8151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Coxsackievirus and adenovirus receptor / Coxsackievirus B-adenovirus receptor / hCAR / CVB3 binding protein


Mass: 13814.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXADR, CAR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P78310

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121HNCA
131CBCA(CO)NH
141HN(CO)CA
151(H)CCH-TOCSY
161HCC(CO)NH
171CC(CO)NH
181HNHA
1913D 15N-EDITED NOESY
11013D 15N-EDITED TOCSY
11112D NOESY
11212D TOCSY
11313D 13C-EDITED NOESY
1142HN(CA)CB
1152HNCA
1162CBCA(CO)NH
1172HN(CO)CA
1182(H)CCH-TOCSY
1192HCC(CO)NH
1202CC(CO)NH
1212HNHA
12223D 15N-EDITED NOESY
12323D 15N-EDITED TOCSY
12422D NOESY
12522D TOCSY
12623D 13C-EDITED NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N90% H2O/10% D2O
2U-13C/U-15N90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM / pH: 3.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., et al.structure solution
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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